Do codecov upload with tests and delay notifcation

.github/workflows/test.yml

@@ -92,8 +92,10 @@ jobs:
           --doctest-modules --ignore=docs
           --ignore=snakebids/project_template --benchmark-disable
 
-      - name: save coverage report
-        uses: actions/upload-artifact@v4
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v4
         with:
-          name: coverage-${{ matrix.python-version }}-${{ matrix.split }}
-          path: ./coverage.xml
+          verbose: true
+          fail_ci_if_error: true
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/upload_coverage.yml

@@ -11,22 +11,12 @@ jobs:
     runs-on: ubuntu-latest
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
     steps:
-      - name: checkout repository
-        uses: actions/checkout@v4
-        with:
-          ref: ${{ github.event.workflow_run.head_sha }}
-      - name: download coverage reports
-        uses: actions/download-artifact@v4
-        with:
-          run-id: ${{ github.event.workflow_run.id }}
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          pattern: coverage-*
-      - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v4
-        with:
-          verbose: true
-          fail_ci_if_error: true
-          override_commit: ${{ github.event.workflow_run.head_sha }}
-          override_pr: ${{ github.event.workflow_run.pull_requests.number }}
+      - name: Setup python
+        uses: actions/setup-python@v5
+      - name: Install codecov
+        run: pip install codecov-cli
+      - name: Send codecov notifications
+        run: codecovcli send-notifications -C "$SHA" -t "$CODECOV_TOKEN"
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          SHA: ${{ github.event.workflow_run.head_sha }}